Jafar's quote "They pick the fruit, they cut the branches, and all that's left is this... shaky stump," Is a reference to the story "The Giving Tree" by Shel Silverstein.
The series was renewed for Season 6 just a few episodes before Season 5 was going to end.
When Mr. Gold mentioned how the cup wasn't chipped, it was a reference to when Belle chipped the cup, starting their love story.
Robert and Emilie's last scene together was the "Beauty and the Beast" dance in season 6. They had to do different takes and on the last one all crew members left the room while the music was still playing, leaving the actors to enjoy their last scene as Rumple and Belle.
When Belle and Mr. Gold are dancing, the song "Beauty and the Beast" from Beauty and the Beast (1991) is playing.